Table 1.

Comparison of CRISPR array visualization tools

	CCTK CRISPRdiff	CRISPRStudio	CRISPRviz
Distinguishing feature	Highlights shared spacers in a small number of related CRISPR arrays	Group and visualize large number of CRISPR arrays from all input assemblies	Interactive exploration of CRISPR arrays through click and drag control of array order
Installation
Source	GitHub, Anaconda	GitHub	GitHub, Docker
Admin/sudo required?	No	Yes	No
Upstream analysis
Require array identification first?	Yes	Yes	No
CRISPR-identification tools	CCTK Minced, CCTK Blast, other with reformatted output	CRISPRdetect only	MinCED only
Input file	.txt array details file	.gff from CRISPRdetect	.fasta assemblies
Determine array orientation	Done by CCTK if specified by user	Done automatically by CRISPRdetect	Not possible
Collapse similar spacers	User-set mismatch threshold	User-set mismatch threshold	Fixed 2 mismatch threshold
Control of plot elements
Array order control	Automatic, manual	Automatic, manual	Automatic
Array order automatic method	Maximize spacers shared between adjacent arrays	Markov clustering	File order
Output format	Any Matplotlib format (PNG, SVG, JPG etc.)	SVG	Screenshot of browser window (PNG)
Plot dimensions	Specify in command line	Resize in graphic design software	Resize in graphic design software
Which arrays are plotted	User specified	All present	All present
Postprocessing of image required	None	Remove unwanted arrays	Remove unwanted arrays, manually reverse spacer order, and reverse complement arrays to identify homologous arrays
Identification of shared spacers
Indication of same spacer	Same color, joined with a line	Same color	Same color, same shape
Color scheme	Built-in, user-specified	Random	Semirandom (DNA sequence converted to numerical RGB values)
Colorblind-friendly	Yes (default color scheme)	No	No
User control of color scheme	Yes (provide color scheme or specify for each spacer)	No	No
Reproducible color scheme	Yes (optional)	Yes (optional)	Yes

CCTK, CRISPR comparison toolkit.